Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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Rank Gene description expected measured Hugo final
Results: HTML CSV LaTeX Showing element 2002 to 2051 of 3206 in total
Rank
description
expected
measured
Hugo
final
2002 0.128294 0.029603 no value 0.230743449
2003 0.406091 0.0937028 TXNDC10 0.230743356
2004 MTO1 PROTEIN HOMOLOG (CGI-02). [SWISSPROT;Acc:Q9Y2Z2] 1.2892 0.297474 MTO1 0.230743096
2005 40S RIBOSOMAL PROTEIN S20. [SWISSPROT;Acc:P17075] 3.6186 0.834926 RPS20 0.230731775
2006 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 1 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 1) (H3-K9-HMTASE 1) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1) (SU(VAR)3-9 HOMOLOG 1). [SWISSPROT;Acc:O43463]" 0.118935 0.027437 SUV39H1 0.230689032
2007 EUKARYOTIC TRANSLATION INITIATION FACTOR 2 SUBUNIT 1 (EUKARYOTIC TRANSLATION INITIATION FACTOR 2 ALPHA SUBUNIT) (EIF-2-ALPHA) (EIF- 2ALPHA) (EIF-2A). [SWISSPROT;Acc:P05198] 3.30114 0.761536 EIF2S1 0.230688792
2008 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 2 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 2) (H3-K9-HMTASE 2) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2) (SU(VAR)3-9 HOMOLOG 2). [SWISSPROT;Acc:Q9H5I1]" 0.14013 0.0323264 SUV39H2 0.230688646
2009 NUCLEOSIDE DIPHOSPHATE KINASE B (EC 2.7.4.6) (NDK B) (NDP KINASE B) (NM23-H2) (C-MYC PURINE-BINDING TRANSCRIPTION FACTOR PUF). [SWISSPROT;Acc:P22392] 2.31472 0.533964 no value 0.230681897
2010 NUCLEOSIDE DIPHOSPHATE KINASE A (EC 2.7.4.6) (NDK A) (NDP KINASE A) (TUMOR METASTATIC PROCESS-ASSOCIATED PROTEIN) (METASTASIS INHIBITION FACTOR NM23) (NM23-H1). [SWISSPROT;Acc:P15531] 2.14316 0.494361 NME2 0.230669199
2011 PUTATIVE NUCLEOSIDE DIPHOSPHATE KINASE (EC 2.7.4.6) (NDK) (NDP KINASE). [SWISSPROT;Acc:O60361] 2.08449 0.480816 NME2P1 0.230663616
2012 40S RIBOSOMAL PROTEIN S2 (S4) (LLREP3 PROTEIN). [SWISSPROT;Acc:P15880] 6.36963 1.469 no value 0.230625641
2013 PROTEIN ARGININE N-METHYLTRANSFERASE 3 (EC 2.1.1.-) (FRAGMENT). [SWISSPROT;Acc:O60678] 0.0860464 0.0198445 PRMT3 0.230625569
2014 60S RIBOSOMAL PROTEIN L23 (L17). [SWISSPROT;Acc:P23131] 2.79016 0.64348 no value 0.230624767
2015 BRCA2 AND CDKN1A-INTERACTING PROTEIN ISOFORM BCCIPALPHA; BRCA2 AND CDKN1A-INTERACTING PROTEIN; CDK INHIBITOR P21 BINDING PROTEIN; BCCIPALPHA; BCCIPBETA; TOK-1ALPHA; TOK-1BETA. [RefSeq;Acc:NM_016567] 0.0725001 0.0167203 BCCIP 0.230624509
2016 PUTATIVE EUKARYOTIC TRANSLATION INITIATION FACTOR 1A (EIF-1A) (EIF- 4C). [SWISSPROT;Acc:O75642] 5.53686 1.27676 no value 0.230592791
2017 "SUCCINATE DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN, MITOCHONDRIAL PRECURSOR (EC 1.3.5.1) (IP) (IRON-SULFUR SUBUNIT OF COMPLEX II). [SWISSPROT;Acc:P21912]" 1.34923 0.311095 SDHB 0.230572252
2018 40S RIBOSOMAL PROTEIN S16. [SWISSPROT;Acc:P17008] 2.56327 0.590899 RPS16 0.230525462
2019 "60S RIBOSOMAL PROTEIN L13, MITOCHONDRIAL (L13MT). [SWISSPROT;Acc:Q9BYD1]" MRPL13
2020 60S RIBOSOMAL PROTEIN L13A (23 KDA HIGHLY BASIC PROTEIN). [SWISSPROT;Acc:P40429] 2.55045 0.587935 RPL13A 0.230522065
2021 "LON PROTEASE HOMOLOG, MITOCHONDRIAL PRECURSOR (EC 3.4.21.-) (LON PROTEASE-LIKE PROTEIN) (LONP) (LONHS). [SWISSPROT;Acc:P36776]" 0.364571 0.0840355 no value 0.230505169
2022 0.535804 0.123498 C11orf79 0.230491
2023 "MAGUK P55 SUBFAMILY MEMBER 3 (MPP3 PROTEIN) (DISCS, LARGE HOMOLOG 3). [SWISSPROT;Acc:Q13368]" 0.490447 0.112993 MPP3 0.230387789
2024 TRANSKETOLASE (EC 2.2.1.1) (TK). [SWISSPROT;Acc:P29401] 0.654499 0.150764 TKT 0.230350237
2025 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, SOMATIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE I). [SWISSPROT;Acc:P08559]" 1.65321 0.38076 PDHA1 0.230315568
2026 0.142004 0.0327033 C3orf23 0.230298442
2027 0.160934 0.0370628 SIN3B 0.230298135
2028 DENSITY-REGULATED PROTEIN (DRP) (DRP1 PROTEIN) (SMOOTH MUSCLE CELL ASSOCIATED PROTEIN-3) (SMAP-3). [SWISSPROT;Acc:O43583] 2.03821 0.469395 DENR 0.230297663
2029 "TRANSCRIPTIONAL CO-REPRESSOR SIN3A; TRANSCRIPTIONAL REGULATOR, SIN3A (YEAST). [RefSeq;Acc:NM_015477]" 0.123075 0.0283438 SIN3A 0.230296973
2030 "PYRUVATE DEHYDROGENASE E1 COMPONENT ALPHA SUBUNIT, TESTIS-SPECIFIC FORM, MITOCHONDRIAL PRECURSOR (EC 1.2.4.1) (PDHE1-A TYPE II). [SWISSPROT;Acc:P29803]" 1.53626 0.353795 PDHA2 0.230296304
2031 PROTEIN TRANSPORT PROTEIN SEC61 GAMMA SUBUNIT. [SWISSPROT;Acc:P38384] 0.499271 0.114962 SEC61G 0.230259719
2032 0.505621 0.116403 no value 0.23021789
2033 TRNA PSEUDOURIDINE SYNTHASE A (EC 4.2.1.70) (PSEUDOURIDYLATE SYNTHASE I) (PSEUDOURIDINE SYNTHASE I) (URACIL HYDROLYASE). [SWISSPROT;Acc:Q9Y606] 2.06115 0.474475 PUS1 0.230199161
2034 2.05907 0.473995 PUS3 0.230198585
2035 0.365653 0.0841705 DARS2 0.230192286
2036 40S RIBOSOMAL PROTEIN S5. [SWISSPROT;Acc:P46782] 4.7257 1.08774 RPS5 0.230175424
2037 CASEIN KINASE I ALPHA S-LIKE. [RefSeq;Acc:NM_145203] 0.389336 0.0896146 CSNK1A1L 0.23017291
2038 "CASEIN KINASE I, ALPHA ISOFORM (EC 2.7.1.-) (CKI-ALPHA) (CK1). [SWISSPROT;Acc:P48729]" 0.395071 0.0909346 CSNK1A1 0.230172804
2039 HUNTINGTIN INTERACTING PROTEIN 1 RELATED (HIP1-RELATED) (HIP 12). [SWISSPROT;Acc:O75146] 0.555396 0.127824 HIP1R 0.230149299
2040 "40S RIBOSOMAL PROTEIN S4, X ISOFORM (SINGLE COPY ABUNDANT MRNA PROTEIN) (SCR10). [SWISSPROT;Acc:P12750]" 3.07604 0.707942 no value 0.230147202
2041 "40S RIBOSOMAL PROTEIN S4, Y ISOFORM 2. [SWISSPROT;Acc:Q8TD47]" 2.90083 0.667613 RPS4Y2 0.23014551
2042 GOODPASTURE ANTIGEN-BINDING PROTEIN (EC 2.7.1.37) (GPBP) (COLLAGEN TYPE IV ALPHA 3 BINDING PROTEIN) (STAR-RELATED LIPID TRANSFER PROTEIN 11) (STARD11) (START DOMAIN-CONTAINING PROTEIN 11). [SWISSPROT;Acc:Q9Y5P4] 0.280961 0.0646597 COL4A3BP 0.230137635
2043 HUNTINGTIN INTERACTING PROTEIN 1 (HIP-I). [SWISSPROT;Acc:O00291] 0.453153 0.104281 HIP1 0.230123159
2044 DNA-DIRECTED RNA POLYMERASE II 14.5 KDA POLYPEPTIDE (EC 2.7.7.6) (RPB9) (RPB14.5). [SWISSPROT;Acc:P36954] 0.479632 0.110371 POLR2I 0.230116006
2045 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM4 (GLYCINE-RICH PROTEIN) (GRP). [SWISSPROT;Acc:Q9Y4Z0] 1.34189 0.308754 LSM4 0.230088904
2046 DNA-DIRECTED RNA POLYMERASE I 40 KDA POLYPEPTIDE (EC 2.7.7.6) (RPA40) (RPA39). [SWISSPROT;Acc:O15160] 6.77601 1.55851 POLR1C 0.230004088
2047 INORGANIC PYROPHOSPHATASE 2 ISOFORM 1. [RefSeq;Acc:NM_176869] 0.538763 0.123888 PPA2 0.229948976
2048 AH RECEPTOR-INTERACTING PROTEIN (AIP) (IMMUNOPHILIN HOMOLOG ARA9) (HBV-X ASSOCIATED PROTEIN 2). [SWISSPROT;Acc:O00170] 0.226516 0.052087 AIP 0.229948436
2049 INORGANIC PYROPHOSPHATASE (EC 3.6.1.1) (PYROPHOSPHATE PHOSPHO- HYDROLASE) (PPASE). [SWISSPROT;Acc:Q15181] 0.557073 0.128098 PPA1 0.229948319
2050 ARYL-HYDROCARBON INTERACTING PROTEIN-LIKE 1. [SWISSPROT;Acc:Q9NZN9] 0.178518 0.0410498 AIPL1 0.22994768
2051 "COMPLEMENT COMPONENT 1, Q SUBCOMPONENT BINDING PROTEIN, MITOCHONDRIAL PRECURSOR (GLYCOPROTEIN GC1QBP) (GC1Q-R PROTEIN) (HYALURONAN-BINDING PROTEIN 1) (P32) (P33). [SWISSPROT;Acc:Q07021]" 2.31678 0.532733 C1QBP 0.229945442

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/